Hi Jason,
I got this message from the installtion team, could you please suggest if something is going wrong:
Here is a snippet from AmberTools/src/Makefile:
parallel: configured_parallel THIRDPARTY
(cd mmpbsa_py && $(MAKE) parallel )
So, when building the parallel Amber the contents of mmpbsa_py are built with the "parallel" target. Let's see what that does, here is a snippet from AmberTools/src/mmpbsa_py/Makefile:
install:
/bin/bash setup.sh $(BINDIR) $(PYTHON)
$(BINDIR)/nab -o mmpbsa_py_nabnmode mmpbsa_entropy.nab
/bin/mv mmpbsa_py_nabnmode $(BINDIR)
$(BINDIR)/nab -o mmpbsa_py_energy mmpbsa_energy.nab
/bin/mv mmpbsa_py_energy $(BINDIR)
serial: install
parallel:
/bin/bash setup.sh $(BINDIR) $(PYTHON) par
You can see that only in the serial version does it copy across "mmpbsa_py_energy".
Regards
Marawan
________________________________
From: Jason Swails <jason.swails.gmail.com>
To: marawan hussain <marawanhussain.yahoo.com>; AMBER Mailing List <amber.ambermd.org>
Sent: Thursday, 3 January 2013 11:43 PM
Subject: Re: [AMBER] MMPBSA error
MMPBSA.py looks for the various programs inside $AMBERHOME/bin, not in the
$PATH (by default, at least). It would seem as though $AMBERHOME is not
set correctly for your parallel calculations.
HTH,
Jason
On Thu, Jan 3, 2013 at 12:11 AM, marawan hussain
<marawanhussain.yahoo.com>wrote:
> Dear AMBER developers,
> I'm trying to run an MMPBSA.py.MPI job but i got the following error:
>
> MMPBSA_Error: Could not find necessary program [mmpbsa_py_energy]
> Error occured on rank 0.
> Exiting. All files have been retained.
>
> I tried to to set the path of the (mmpbsa_py_energy) program explicitly in
> the script but this didn't solve the problem.
>
> export PATH=/lustre/projects/p012_swin/mahmed/HER2/pbsa_test:$PATH
>
>
>
> I'm noticing that the serial version has the program in ($AmberTools/bin)
> but the parallel version does't have it
> We tried to re-install MMPBSA by "make install" or "make parallel" but
> this didn't solve the problem.
> Any suggestion will be appreciated
>
> Regards
> Marawan
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Thu Jan 03 2013 - 15:30:02 PST
